Accidents Can Happen
by sothernqt
Summary: There is an accident on Atlantis that leads to an overwhelming outcome. Mainly John/Elizabeth, definately Sparky.
1. Chapter 1

_A/N- This is my first Atlantis fic to post, but I have written other fics for other shows. It takes place early third season, I guess. The story really doesn't need a specific place in the show. Hope you enjoy._

**-Atlantis- The Infirmary-**

"I said I was sorry." McKay huffed as he glared over at a very ticked off Lt. Colonel John Sheppard. John didn't say anything, he just continued staring at Rodney. "Look, what do you want me to say? How was I supposed to know that you would activate the stupid machine." Rodney crossed his arms over his chest and raised an eyebrow. "You know, it is actually your own fault."

"My fault?" John asked shocked. "How is it my fault?"

"Well, if you didn't have the ancient gene, then the machine wouldn't have activated." Rodney shot back. He sat back in his chair, proud that he had found a way to put the blame on someone else.

John stared at Rodney and sighed, he knew it was useless to continue this argument. He tried to sit still as Carson continued to poke and prod him. John chanced a glance over at Elizabeth, who was sitting one bed over being examined by some of the infirmary nurses. John could tell that Elizabeth was not amused by the two "gentlemen's" arguments. She too had been affected by the activation of the mysterious Ancient device and was now under the scrutiny of Dr. Carson Beckett. Elizabeth shot John a sideways glance, and he gave her a quick "please forgive me" smile; however, she did not return it. John tried to relax and allowed his mind to wander. Elizabeth was too worried about the implications of said device to let her mind wander. The last time something like this had occurred they had almost lost Rodney. She bit her bottom lip in anxiety, and furrowed her brow as she wondered what the consequences of this device would be. Her thoughts were interrupted by Carson's curiosity. "So, what exactly happened?"

"Oh you know, Atlantis' foremost scientist just had to turn on some random gadget." John growled.

"Please, like you wouldn't have done the same thing." Rodney groaned out. "I found a terminal of sorts and asked the Colonel to step up to it, hoping his gene would allow him to turn it on."

"But you have the gene too." Carson said confused as he handed the full viles of blood to a lab tech.

Rodney nodded and waved off Carson's comment. "Yes I do, but it still wouldn't turn on. I thought maybe the Colonel's 'super' gene would allow him to access the information."

"I'm guessing it did." Carson said as he folded his arms across his chest.

Rodney glared at Carson for interrupting him again. "Yes, yes, yes, the console lit up and the screen in front of it glowed with Ancient text…so…"

"But how did Elizabeth get involved?" Carson interrupted once more and glanced over at Elizabeth. She had remained silent during the whole conversation.

"Carson I swear if you interrupt me one more time…"Rodney said agitatedly.

"Rodney called me down to translate the text. When I arrived Colonel Sheppard was standing on the platform. I stepped onto the platform next to him, and then the console glowed and the text began to scroll across the screen extremely fast." Elizabeth slowly explained. She had decided it was time to join the conversation, seeing as it was going nowhere fast.

"After Elizabeth stepped up to the console, light wrapped around her and Sheppard, and then appeared to fill Elizabeth's body." Rodney finished his explanation, feeling somewhat deflated because he had not been allowed to explain the whole story.

Carson nodded and rubbed a hand across his face. "Correct me if I'm wrong here, but the last time something like this happened didn't you almost ascend?" He asked Rodney.

"Eh…" Rodney made a face and continued. "Yes, but this was different. I don't think that they Ancients would make two of the same device."

"As of right now we have no idea what is going to happen to me or Elizabeth." John said as he turned to face her. "Feeling any sudden urges to Ascend yet?"

Elizabeth shook her head, "Nope. However I do have the urge to go get some sleep." She turned and looked at Carson. "Can we go now?"

"I guess so. I can't rightly keep you, until I know something is wrong with you." Elizabeth hopped off of the bed and began to leave, but was halted by Carson's firm hand on her arm. "If you notice anything different, come back." Elizabeth nodded and tried to leave, but was still unable to move. "I mean it. Anything out of the ordinary and you let me know."

"Alright." She said softly. "I promise if I start feeling the need to become a bug then I will come down here."

"Oh, that was low. I thought we agreed never to mention that again." John groaned as he followed her out of the infirmary. "Besides that was completely different."

"Well, I am headed back down to the lab to try and determine what is going to happen to them." Rodney said as he stood from his chair. He received a wary look from Carson, and shrugged. "Hey, I'm not saying that anything will happen, but with Sheppard's luck…" he never finished his sentence, but Carson could only imagine what lie in store for the Colonel and the doctor.

**-1 month later-**

Elizabeth sighed as she rubbed her tired eyes. She had been reading reports for the last three hours, and didn't remember half of what she had signed off on. Most of the reports were from the science teams, and although she appreciated their attention to detail, sometimes the scientists became a little…long winded. Elizabeth decided to call it a night, and closed her laptop. She had been feeling extra tired lately, and assumed it was due to the fact that the IOA had been spending more time on Atlantis than usual. Mr. Woolsey was making his trips to Atlantis more frequent than Elizabeth would have liked. Elizabeth reached her room and happily changed into a pair of flannel pajama pants and a dark blue tank top. She sighed contentedly as she snuggled underneath her warm blankets. Just as she was about to remove her ear piece, it chirped to life. "Elizabeth," Came Rodney's loud voice. Elizabeth considered ignoring the hail, but changed her mind when Rodney threatened to come get her if she didn't answer her com. "What do you need Rodney?"

"You need to come down to my lab." He said hastily.

"Can't it wait until morning?" She asked as she tried to stifle a yawn.

"I have been working on translating the information from the device that you and the Colonel activated."

"Rodney, I thought we decided that it must have been broken. It has been a month and nothing has happened to me or John."

"Not yet." Rodney said softly. "Look you need to come down here right now."

Elizabeth huffed and threw the covers back. "Let me change; I'll be there in ten minutes."

"Now, Elizabeth." Rodney demanded and turned off his com.

Elizabeth's heart began to race. What could be so horrible that Rodney would demand her presence? She slipped her feet into her flip flops, and pulled a light blue zip up jacket on her exposed skin. She snuck out of her room and into the nearest transporter, hoping no one saw her like this. After the transporter doors opened, Elizabeth stepped out and met John at the door of Rodney's lab. John took in her appearance and smiled. "Not a word." She commanded.

John held his hands up in mock surrender. "I didn't say a word." John gave her a big smile and pointed at her pants. "Just never guessed you were a flannel gal." Elizabeth gave him a glare, warning him to back off. John chuckled to himself and followed her into Rodney's lab.

"Took you guys long enough." Rodney huffed as he ushered them into the room. " Like I said, I've been going over the data for the past month and nothing."

"Until now…" John said as he stood next to Elizabeth.

"Yes." Rodney paused and looked at Elizabeth. "You wear flannel?" John made a cutting motion across his throat, trying to tell Rodney to drop it, and started to rub his neck when Elizabeth turned to glare at him.

"Get to the point Rodney." Elizabeth said as she scooted closer to the scientist.

"Well, according the information, the Ancients were facing many problems, one of which was reproduction. It seems that many of the Ancient women were having problems conceiving. So to avoid distinction the Ancients attempted to make a device that would allow the women to conceive." Rodney stared at Elizabeth and John, but got no response. He sighed and continued, "They created a form of in vitro-fertilization."

Elizabeth's eyes widened. She did not like where this conversation was headed. "What are you saying?"

Rodney took a deep breath and tapped his fingers nervously on the table. "Based on what this machine does…I think…actually, I am pretty sure that you are pregnant." There he had said it! Now, he had to deal with what they would say.

"What?" John asked shocked. "How? I mean I know how it usually happens, but…" He stammered trying to find the right words.

"Well, when you stepped up to the console you did indeed activate it, we just didn't know it. The machine sensed your strong Ancient gene, but it could not perform its intended task without woman standing next to you. When Elizabeth stepped onto the platform the machine registered her existence and carried out its task. The device does what scientists do in a lab with sperm and eggs, but it automatically placed the…the baby…in Elizabeth. That is what all the light was, and why it only returned to her." Rodney stared over at Elizabeth and watched as she visibly paled.

"So you are saying that I made a baby without my knowing it?" John asked exasperated.

Rodney nodded. "Yes. This baby will contain both yours and Elizabeth's DNA, just as if it had been conceived naturally."

"But it wasn't." John stressed each word, growing in volume as he neared the end of his statement.

"I know that Colonel, I am just telling you what I learned." Rodney yelled back.

"Stop." Elizabeth said firmly. She licked her lips and tried to steady her shaking hands. "Did you learn anything else?" Rodney shook his head 'no.' Elizabeth nodded, "I am going to ask Carson to run some tests, just to be sure. For the moment we don't even know if your hypothesis is correct." Rodney looked up at her angrily. "I know what you said, but I want to be on the safe side. If I am…" She took a deep breath. "If the test is positive, then we will move on from there."

_A/N- Well what do you think? I have some chapters written, but it is not finished. They will be more like glimpses that tell a story, than a day to day story. If that makes any sense. Please review and tell me if you like it so far._


	2. Making Lemonade

A/N-Here is the next part...hope you enjoy it. Thanks so much for the reviews. And oh, I don't own any of the characters relating to Stargate Atlantis. There we go. Sorry if the characters seem out of character. I felt like this one was hard to do.

**-Atlantis Infirmary-**

Elizabeth bit her bottom lip, and fidgeted on her bed. 'I'm pregnant.' She thought to herself as she waited for the results of her blood work. She had not received a definitive yes or no, but deep down she knew. Elizabeth's heart raced, and her breathing became labored. She could feel herself losing control of her body. 'What! I have already lost control of my body! I am pregnant and I didn't even get to have sex. Well, it would have been nice to at least enjoy getting pregnant, especially if it was with…' Elizabeth shook her mind out of its dirty thoughts. She nervously played with the bedsheet and bounced one leg up and down. "Elizabeth…" Carson asked hesitantly. Elizabeth jerked her head up, and tried to give him a small smile. "Are the results in?" She asked cutting to the chase. Carson nodded, but said nothing. "I'm ready." Elizabeth said as she steadied her hands and legs. Carson nodded, "I don't know if it's congratulations I should tell you…" Carson laid a kind hand on her arm. " But congratulations Elizabeth. You're pregnant." Elizabeth nodded, meaning she understood what he had said, but her eyes showed she had yet to process his statement. "Thank you Carson." She said as she stood and made to leave the room.

"Elizabeth," Carson called out to her. She stopped, but did not turn around. "Are you alright? Would you like me to come with you to tell Colonel Sheppard?" Elizabeth's shoulders sagged further, she had not even thought about what she was going to tell John. What were they going to do? Would they tell the IOA? Would they become more, for the sake of the baby? Would she even keep the baby? Elizabeth knew that she could never abort a baby; she had dealt with too much of that during her stay in foreign countries. She had seen the innocent lives that were taken in anger and revenge, seen the children's bodies strewn throughout the dirty streets, seen the mothers and fathers who would have done anything for a child. Even if she didn't want the baby, someone would.

"Elizabeth, lass I think you should sit down." Carson took her shoulders and tried to lead her to a nearby chair, but she pulled away from him.

"Carson I have to tell the Colonel." She put on her mask and smiled at him. "Do I need to come by for more checkups tomorrow?"

Carson could see she was shutting him out; she was shutting down. He could not imagine how afraid she must feel, how violated. She was pregnant, by her second in command, meaning if the IOA found out it could possibly end her career on Atlantis, not to mention the dangers that would face a child on Atlantis. If all of these thoughts were surging through his head, he could just imagine what they must be doing in hers. Instead of confronting her about it, he just decided to let it slide for now. "Yes, actually I'll need you to come in tomorrow for a full workup. When we determine the DOC, then we will know a rough estimate of your due date." He gave her a warm smile and softly squeezed her shoulder.

"We know when it was conceived, June 26." Elizabeth said with disdain. "I'll see you tomorrow Carson."

"Aye, and for what it's worth, congratulations. Having a baby is a miracle, no matter how it was conceived." Carson said softly as he went back to his work. Elizabeth nodded, but said nothing as she left the infirmary.

-John's room-

Elizabeth paced outside in the dark hallway. Should she just barge in and tell him she was pregnant? What would she say after that? Would she… "Are you going to come in?" John asked staring at her from his doorway.

Elizabeth glanced up at him, and without a word she walked into his room. Just as his doors shut she turned around to face him, "I'm pregnant." She said quickly. His back was still to her when the bomb had been dropped. Elizabeth felt that if she sat still, then she would bust. She walked around his room, biting her lower lip. John turned around and sat down on his bed. After a few moments of silence, Elizabeth could take no more. "Would you just say something." She said desperately.

John stared up at her. He had never seen her so unnerved. He could feel her fear, causing his fear to increase. "What am I supposed to say?" He asked softly, hoping it did not sound snippy in any way.

Elizabeth turned around to face him, "You could at least say congratulations…wait, no, don't say that." Elizabeth sighed. "I don't know what I want you to say, just say…anything…!" Elizabeth stood facing him, waiting for his statement.

John thought for a moment, "Anything." He smiled proudly at himself.

"John be serious for once in your life." Elizabeth snapped.

John's temper began to rise. He stood and looked at her. "I am being serious Elizabeth; I don't know what to say."

Elizabeth ran a frustrated hand over her face, "Then just don't say anything." She turned to leave, but stopped. "I only came to tell you I was pregnant, because I thought you had a right to know that I was carrying your child. I know it is a lot to take in right now, but I just need a friend to talk to. Goodnight Colonel." Elizabeth turned to leave, but John stopped her.

"Wait a minute; I am not going to let you leave until you talk to me." He said firmly as he pulled her over to his chair. Elizabeth slumped in the chair, and jerked her arm away from him. John stared at her, waiting for a reply to his prompt, but nothing. He ran a frustrated hand over his face. "God, Elizabeth why are you being like this? This isn't you."

Elizabeth glared up at him, "You don't even know me." John rolled his eyes and started to say something, but she stopped him. "What are my parents' names? Where did I go to high school? How many countries have I visited? What…"

"Those are just details Elizabeth. I know you. And I thought I was your friend." John said exasperated. He sat down on the edge of his bed and sighed. He glanced over and stared at her face, that is when it hit him. "I'm scared too." He said softly. Elizabeth jerked her head up and looked at him. She thought she had been hiding her fear. Her anger had been her only protection, hiding her true feelings. John watched as her façade melted away, leaving an exposed Elizabeth. "What are we going to do?" He asked her gently.

Elizabeth sighed and wrapped her arms around her body, suddenly feeling cold. "I don't know." She looked down at the floor, and up at John. "I just know that we can't keep the baby."

John stared at her, shock clearly written across his features. "What?" He asked as he stood up angrily. "There is no way in hell I am going to let you abort my child."

Elizabeth rose to meet his level and glared at him. "If you knew me as well as you presumed, then you would know that I could never do that, no matter whose child it was." She spat angrily. "I meant that I thought about seeing if an Athosian family would adopt it. The child would be safer with them than here on Atlantis." Elizabeth took a deep breath and continued, "I…I am going to need some time to think this over. I have never dealt with this kind of situation before."

John nodded and touched her arm. "I will support your decision."

Elizabeth felt a wave of relief flood her body. She had been worried that she was going to have to fight John about the whole situation, simply knowing that he would support her, made all the difference in the world. "Thank you." She said softly. "Well, I better be off to bed." She glanced down at her watch. "I might get three hours of sleep, if I'm lucky." John nodded and moved to let her pass. Elizabeth stopped at the door, her heart telling her that she could not leave things between them like this. "John," She turned to face him. "You are my closest friend. I've never really had any good friends like you." She glanced down at her feet, "I'm sorry…for what I said."

John was taken aback by this sudden change of emotion. He opened his mouth, but closed it and settled on just nodding his thanks. Elizabeth gave him a swift nod, and then quickly left. John sighed and fell back onto his bed. He was going to be a father. He could not help but smile. He had always wanted to be a dad, but he had never pictured it happening like this. John's smile faded as he thought about what Elizabeth had told him. She wanted to give the baby away, he understood her motives, but he still wished that she wanted to keep the baby. It was his baby, their baby. John's thoughts slowly dissipated, leaving his body open to sleep. His eyes closed and he gave in to the desired rest. Tomorrow he would talk to Elizabeth; tomorrow he would try and convince her to keep their child.

**-2 Months Later- Elizabeth's Office-**

Elizabeth sat at her desk and continued to read through the monotony of reports. This was the part of the job that she hated, the mundane paperwork. Elizabeth leaned back, taking a break from reading the latest of Rodney's reports on his many discoveries. The past two months had flown by, being consumed with missions, meetings, and reports. She stared down at her lap, and touched her slightly protruding stomach. She was just beginning to show, and that made her anxious. She was afraid that her staff would lose respect for her, or that somehow the IOA would find out. She had managed to steer clear of telling them the "wonderful news", and hoped she could avoid the confrontation for just a little longer. Confrontation, definitely something she had not managed to avoid with Sheppard. He had tried to convince her on multiple occasions that keeping the baby would be the best option. However, she had shot him down every time, and now they had refrained from speaking to each other unless it was critical. Elizabeth hated not being able to talk to him, but this was how it had to be. She had found a loving Athosian family who were more than willing to adopt the baby, and in six months they would have it. Deep down Elizabeth wanted nothing more than to keep the child, but she convinced herself it would be impossible. How could she protect a baby from the Wraith, how could she keep up her job and still be a good mother? Most of all she wondered if being the mother of John Sheppard's child would expose her heart too much. She cared deeply for John, but those feelings could never culminate in anything more than friendship. She had a city to run, and her emotions would merely get in the way. As it was she had already compromised herself and the city more than once based on her feelings for the messy haired colonel. Raising his baby would only make that situation worse. This was how she convinced herself that giving the child away was her best option. Just as Elizabeth began to read Rodney's report once more, her radio crackled to life. "Dr. Weir," she heard John's voice flit across the radio. She tapped her earpiece, "Yes, Colonel."

"Could you meet me in my quarters? I have to…discuss a situation with you. It is regarding some of the personnel." His voice sounded firm and unwavering.

"Yes, I'll be right down." She said with pure professionalism. Elizabeth stood and headed to John's quarters. Once she reached his quarters, the door swooshed open before she had a chance to raise her hand to the panel. "Colonel, I was just about to…" Elizabeth never finished her sentence, and was quickly whisked into John's room.

John turned to face her and set his glare. "I know I have tried this argument before, but here goes. I don't want you to give up the baby. I want to keep it and raise it here with us. I know that it will be difficult, that we will have to make sacrifices, but Elizabeth…" John's voice softened as he said her name. "Please, this is my baby too, and I want to raise it."

"John, how many times do we have to go over this?" She asked angrily.

"Apparently a lot, because I still don't understand why you refuse to consider keeping the baby." He said frustrated.

"Because it is not an option!" She yelled. "Do you really think the IOA will let us keep our jobs and the baby?" She waited for a response but got none. "Let's say they let us keep our jobs, we're talking hypothetically here, how are we going to work the hours we work and raise a baby? How can we ask a child to grow up, never knowing if either of their parents could be killed at any given moment? How can we do that John?" Elizabeth sighed, knowing where this conversation was headed. It always ended the same way, she was angry and he was hurt.

"Elizabeth, I don't know how we would do it, but we have to." He pleaded with her. "How can you not want to keep your own child?"

This comment struck a nerve in her, and rage was released. "Because I never asked for this." She said pointing at her stomach. "I never asked to be pregnant! My life is going to change, no matter what I do. If I give the baby away, then you will never forgive me, but if I keep it then I risk losing the one thing that has remained a constant for me. I feel as if my body has been violated! I feel despicable, almost as if this child is something disgusting, something that needs to be erased. But as soon as I have these thoughts, I think about what it will look like." She paused, her tone softening. "Will it look like you, will it be like me? And in that moment…" Elizabeth tried to clear her throat, and push the emotions and tears away. "In those brief moments I think, maybe, just maybe we could do it, but then I remember who we are and where we are. Children should be made out of love, not machines." Elizabeth stopped and looked down at her twitching hands. She had never been this open with anyone.

John took in all that she had said and gently touched her arm; suddenly feeling things he had never felt before. Was it love? When he looked at her, he saw so much more than just a good leader, he saw a beautiful woman. "I feel as scared as you. I never asked for this either. But, I have learned throughout my many years that when life gives you lemons you gotta suck it up and make lemonade, because if you don't you will be sour the rest of your life." Elizabeth smiled at his analogy. "I can't imagine how you must feel, but know that I feel violated as well. My DNA was used to make a child I had no say in making. I am going to be a father, whether or not we keep the baby. I will always want to see my child, to hold it, to know if it looks like me, even if it is not here." John took her hands in his own and squeezed them tight. "I know this won't be easy, and that a lot of things will change, but I think…I know… we can do this." John stopped and stared at her. "Please, Elizabeth…will you…" He could not put his words together; frankly he was surprised that he had been coherent this whole time. Usually he stumbled over his words, and stuttered out his jumbled feelings.

"Okay," Elizabeth said softly as she looked up into his hazel eyes. She felt something inside of her begin to warm, and feelings she had never felt before began to explode. Was this what love was? Not the sexual love that was commonly felt, but true love. "Let's make some lemonade." She said with a small smile.

John's eyes grew wide with excitement. "Really?" Elizabeth nodded, as her smile grew bigger. "Wow! I never thought my speech would really work." Elizabeth rolled her eyes and smiled. John laughed and pulled her into a tight hug, surprising both himself and Elizabeth with this display of emotion. He pulled back and looked at her, "So before we have this baby I want to know something…where did you go to high school?" Elizabeth smiled at him and laughed. This was what she had missed the past few months, her best friend.

A/N- Well, you know what to do. Review, review, review!


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